We present some considerations related to the implementation of a methodology for development of software tools for intelligent (more precisely, semantics oriented) search in repositories of digitized manuscripts. This methodology is oriented to the construction of proper ontologies relevant to the domain(s) of the user queries and some intelligent agents for search and query processing purposes. The main features of the Web Ontology Language (OWL) and the open ontology development environment Protégé are analyzed from the point of view of their applicability in building software tools for intelligent search. The conclusion is that the OWL Plugin of Protégé is an excellent instrument for the development of tools for semantics oriented search in digitized collections of manuscripts.